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NM_000083.3(CLCN1):c.1392C>T (p.Phe464=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 12, 2020
Accession:
VCV000289005.13
Variation ID:
289005
Description:
single nucleotide variant
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NM_000083.3(CLCN1):c.1392C>T (p.Phe464=)

Allele ID
273242
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
7q34
Genomic location
7: 143332864 (GRCh38) GRCh38 UCSC
7: 143029957 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000007.13:g.143029957C>T
NC_000007.14:g.143332864C>T
NG_009815.1:g.21739C>T
NM_000083.3:c.1392C>T MANE Select NP_000074.3:p.Phe464= synonymous
Protein change
-
Other names
-
Canonical SPDI
NC_000007.14:143332863:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00009
Trans-Omics for Precision Medicine (TOPMed) 0.00014
The Genome Aggregation Database (gnomAD) 0.00010
The Genome Aggregation Database (gnomAD), exomes 0.00013
Exome Aggregation Consortium (ExAC) 0.00009
The Genome Aggregation Database (gnomAD) 0.00014
1000 Genomes Project 0.00020
Links
ClinGen: CA4537336
dbSNP: rs201919331
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 12, 2020 RCV001084293.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001161643.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Nov 5, 2020 RCV000513242.8
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLCN1 - - GRCh38
GRCh37
640 685

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 28, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000343272.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Oct 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000609280.11
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Myotonia congenita
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001323536.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Nov 12, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital myotonia, autosomal recessive form
Congenital myotonia, autosomal dominant form
Allele origin: germline
Invitae
Accession: SCV000759753.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Nov 05, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000724931.2
Submitted: (Sep 23, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CLCN1 - - - -

Text-mined citations for rs201919331...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 04, 2021